[gmx-users] Topology for Ligand

[Justin Lemkul]

On 1/15/17 6:26 AM, RAHUL SURESH wrote:
> In MDS for a protein-Ligand complex using OPLSA force field, I have framed
> the topology file using Swissparam. Is that okay if  I directly use them to
> the rtp file or is there any other steps to be taken before that.?
>

SwissParam makes topologies that are compatible with CHARMM, not OPLS.  If you 
can come up with a correct topology, follow 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 
if needed.  Most servers provide a standalone topology, so you don't need to be 
doing any sort of .rtp hacking.  The parameters you need are in that ligand 
topology (usually, but it does depend on the server and what it gives you).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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